Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B.
 

Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B.

Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B.

Chemistry. 2020 May 25;:

Authors: Monaco S, Walpole S, Doukani H, Nepravishta R, Nepravishta R, Martínez-Bailén M, Carmona AT, Ramos-Soriano J, Bergström M, Robina I, Angulo J, Angulo J, Angulo J

Abstract
Ligand-based NMR techniques to study protein-ligand interactions are potent tools in drug design. STD NMR stands out as one of the most versatile, allowing screening of fragments libraries and providing structural information on binding modes. Recently, we have shown that a multi-frequency STD NMR approach, DEEP-STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, we have expanded the approach by what we call DEEP-STD NMR fingerprinting to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, we present the synthesis of a set of new ligands which have been subject to a thorough study of their interactions with CTB by WAC and NMR. Remarkably, the combination of DEEP-STD NMR fingerprinting and Hamiltonian Replica Exchange Molecular Dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi-subsite binding pockets. In the particular case of CTB, it allowed to reveal the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket, paving the way to the design of novel leads for inhibition of this relevant toxin.


PMID: 32449563 [PubMed - as supplied by publisher]



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